3TFX | pdb_00003tfx

Crystal structure of Orotidine 5'-phosphate decarboxylase from Lactobacillus acidophilus

PDB DOI: https://doi.org/10.2210/pdb3TFX/pdb

Classification: LYASE
Organism(s): Lactobacillus acidophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-08-16 Released: 2011-09-28
Deposition Author(s): Satyanarayana, L., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.252 (Depositor), 0.210 (DCC)
R-Value Work:
0.205 (Depositor), 0.205 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Orotidine 5'-phosphate decarboxylase from Lactobacillus acidophilus

Satyanarayana, L., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 57.74 kDa
Atom Count: 3,744
Modeled Residue Count: 455
Deposited Residue Count: 518
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	259	Lactobacillus acidophilus	Mutation(s): 0 Gene Names: LBA1386, pyrF, pyrF/LBA1386 EC: 4.1.1.23
UniProt
Find proteins for Q5FJB3 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM)) Explore Q5FJB3 Go to UniProtKB: Q5FJB3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5FJB3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.252 (Depositor), 0.210 (DCC)
R-Value Work: 0.205 (Depositor), 0.205 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.396	α = 90
b = 68.17	β = 106.31
c = 63.93	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-09-28

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2011-09-28
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary